feat: Add option to force-add annotations

Will turn off looking for duplicate annotations and simply add all.
test: Add poetry-cov library
2023-10-17 22:01:41 +02:00 · 2023-10-17 21:16:40 +02:00 · 2023-10-12 19:27:16 +02:00 · 2023-10-12 19:26:41 +02:00 · 2023-09-22 21:53:55 +02:00 · 2023-09-22 21:49:52 +02:00
12 changed files with 643 additions and 248 deletions
--- a/.markdownlint.yaml
+++ b/.markdownlint.yaml
@ -0,0 +1,6 @@
 MD013: false
 MD025: false
 MD007:
  indent: 4
--- a/.papis.config
+++ b/.papis.config
@ -0,0 +1,7 @@
 [settings]
 default-library = main
 picktool = papis
 formater = python
 [main]
 dir = temp/lib
--- a/README.md
+++ b/README.md
@ -8,10 +8,10 @@
 Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\
 Easily organize all your highlights and thoughts next to your documents and references.\
-## Installation:
+## Installation
 <!-- TODO set up pypi repository / explain git install path -->
-You can install from pypi with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`.
+You can install through pip with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`.
 That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global),
 everything should now be set up.
@ -24,7 +24,8 @@ You will be set up with the default options but if you want to change anything,
 > **Note**
 > This plugin is still in fairly early development. It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options.
-## Usage:
+
 ## Usage
 `papis extract [OPTIONS] [QUERY]`
@ -87,16 +88,44 @@ On my current laptop, extracting ~4000 annotations from ~1000 library documents
 though this will vary with the length and size of the PDFs you have.
 For smaller workloads the process should be almost instant.
 You can change the format that you want your annotations in with the `--template` option.
 To output annotations in a markdown-compatible syntax (the default), do:
 ```bash
 papis extract --template markdown
 ```
 There are sub-variants of the formatter for atx-style headers, with `--template markdown-atx` (`# Headings`),
 or setext-style with `--template markdown-setext` (the default style).
 To instead see them in a csv syntax simply invoke:
 ```bash
 papis extract --template csv
 ```
 And if you only want to know how many annotations exist in the documents, you can invoke:
 ```bash
 papis extract --template count
 ```
 For now, these are the only formatters the plugin knows about.
 Be aware that if you write to your notes using a different template the plugin will *not* detect old annotations and drop them,
 so you will be doubling up your annotations.
 ## Configuration
 ### Basic configuration
 Add `extract` plugin settings to your papis `config` file (usually `~/.config/papis/config`):
 You will rarely have to set everything explained in the next few paragraphs -
 in fact you can use the plugin without having to set up any of it if you are happy with the defaults.
 The full default settings look as follows:
-```yaml
+```conf
 [plugins.extract]
 on_import: False
 tags = {"important": "red", "toread": "blue"}
@ -107,7 +136,7 @@ minimum_similarity_color = 0.833  # for matching tag to color
 ### Automatic extraction
-```yaml
+```conf
 [plugins.extract]
 on_import: True
 ```
@ -119,16 +148,16 @@ if `False` extraction only happens when you explicitly invoke it.
 Extraction will *not* happen automatically when you add new annotations to an existing document,
 regardless of this setting.
-#### Automatic tagging
+### Automatic tagging
-By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`, 
+By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`,
 you can enable automatic tagging for your annotations.
-You thus ascribe specific meanings to the colors you use in highlighting. 
+You thus ascribe specific meanings to the colors you use in highlighting.
 For example, if you always highlight the most essential arguments and findings in red and always highlight things you have to follow up on in blue, you can assign the meanings 'important' and 'todo' to them respectively as follows:
-```yaml
+```conf
 [plugins.extract]
 tags = {"red": "important", "blue": "toread"}
 ```
@ -140,14 +169,14 @@ no defaults are set here.
 ### Advanced configuration
-```yaml
+```conf
 [plugins.extract]
 minimum_similarity: 0.75,  # for checking against existing annotations
 minimum_similarity_content: 0.9,  # for checking if highlight or note
 minimum_similarity_color: 0.833,  # for matching tag to color
 ```
-`minimum_similarity` sets the required similarity of an annotation with existing annotations in your notes to be dropped. 
+`minimum_similarity` sets the required similarity of an annotation with existing annotations in your notes to be dropped.
 Annotations you have in notes might change if you for example fix small spacing mistakes or a letter/punctuation that has been falsely recognized in the PDF or change similar things.
 Generally, this should be fine as it is but you should change this value if you either get new annotations dropped though they should be added (decrease the value) or annotations are added duplicating existing ones (increase the value).
@ -177,10 +206,12 @@ Known issues to be fixed:
 - [x] Speed?
    - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations
 - [x] ensure all cmdline options do what they should
- [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
+- [x] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
- [ ] docstrings, docstrings!
+- [x] docstrings, docstrings!
 - [ ] testing testing testing!!
    - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation)
 - [ ] dependency injection for extractor/exporter/formatter/annotation modules
    - [ ] any call to papis.config should start from init and be injected?
 features to be implemented:
@ -188,7 +219,7 @@ features to be implemented:
    - [x] static analysis (lint, typecheck etc) on pushes
    - [x] test pipeline on master pushes
    - [ ] release pipeline to pypi on tags
- [ ] add page number if available
+- [x] add page number if available
    - exists in Annotation, just need to place in output
 - [ ] show overall amount of extractions at the end
 - [ ] custom formatting decided by user
@ -201,7 +232,8 @@ features to be implemented:
 - [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)})
 - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note
 - [ ] `--force` mode where we simply do not drop anything
- [ ] `--format` option to choose from default or set up a custom formatter
+- [x] `--format` option to choose from default or set up a custom formatter
    - called `--template` in current implementation
 - [ ] on_add hook to extract annotations as files are added
    - needs upstream help, 'on_add' hook, and pass-through of affected documents
@ -219,12 +251,36 @@ This plugin makes an effort to find the right combination and extract the writte
 as well as any additional notes made - but things *will* slip through or extract weirdly every now
 and again.
-The easiest extraction is provided if your program writes the selection itself into the highlight
+Secondly, a note on the pages: I use the page number that the mupdf library gives me when it
-content, because then we can just use that. It is harder to parse if it does not and will sometimes
+extracts anything from the pdf file. Sometimes that number will be correct for the document,
-get additional words in front or behind (especially if the highlight ends in the middle of a line)
+sometimes it will however be the number of the *pdf document* internally. This can happen if
-or even cut a few off.
+e.g. an article or a book has frontmatter without numbering scheme or with a different one.
 Sometimes the correct pages will still be embedded in the pdf and everything will work,
 others it won't. So always double check your page numbers!
-I am not sure if there is much I can do about this.
+I am not sure if there is much I can do about these issues for now.
 ## For developers
 and for myself whenever I forget. The basic building blocks currently in here are three:
 - extractors
 : Extract data from a source file attached to a papis document.
 - annotations
 : The actual extracted blocks of text, containing some metadata
  info as well, such as their color, type, page.
 - exporters
 : Put the extracted data somewhere. For now stdout or into your notes.
 - formatters
 : Make sure the exporter saves the data according to your preferred layout,
  such as a markdown syntax or csv-structure.
 Splitting it into those three building blocks makes it easier to recombine them in any way,
 should someone want to save highlights as csv data in their notes,
 or should we ever include more extractors than the one for PDFs.
 ---
--- a/papis_extract/init.py
+++ b/papis_extract/init.py
@ -8,7 +8,10 @@ import papis.strings
 from papis.document import Document
 from papis_extract import extractor, exporter
-from papis_extract.annotation_data import AnnotatedDocument
+from papis_extract.formatter import (
    Formatter,
    formatters
 )
 logger = papis.logging.get_logger(__name__)
@ -28,41 +31,54 @@ papis.config.register_default_settings(DEFAULT_OPTIONS)
@click.help_option("-h", "--help")
@papis.cli.query_argument()
@papis.cli.doc_folder_option()
-@papis.cli.git_option(help="Add changes made to the notes files")
+@papis.cli.git_option(help="Commit changes made to the notes files.")
@papis.cli.all_option()
@click.option(
    "--manual/--no-manual",
    "-m",
    help="Open each note in editor for manual editing after extracting its annotations",
 )
@click.option(
    "--write/--no-write",
    "-w",
-    help="Do not write annotations to notes only print results to stdout",
+    help="Do not write annotations to notes only print results to stdout.",
 )
@click.option(
    "--manual/--no-manual",
    "-m",
    help="Open note in editor for manual editing after annotation extraction.",
 )
@click.option(
    "--template",
    "-t",
    type=click.Choice(
        ["markdown", "markdown-setext", "markdown-atx", "count", "csv"],
        case_sensitive=False,
    ),
    help="Choose an output template to format annotations with.",
 )
@click.option(
    "--force/--no-force",
    "-f",
    help="Do not drop any annotations because they already exist.",
 )
 def main(
    query: str,
    # info: bool,
    # _papis_id: bool,
    # _file: bool,
    # notes: bool,
    # _dir: bool,
    # _format: str,
    _all: bool,
    doc_folder: str,
    manual: bool,
    write: bool,
    template: str,
    git: bool,
 ) -> None:
-    """Extract annotations from any pdf document
+    """Extract annotations from any pdf document.
    The extract plugin allows manual or automatic extraction of all annotations
-    contained in the pdf documents belonging to entries of the pubs library.
+    contained in the pdf documents belonging to entries of the papis library.
    It can write those changes to stdout or directly create and update notes
    for papis documents.
    It adds a `papis extract` subcommand through which it is invoked, but can
-    optionally run whenever a new document is imported for a pubs entry.
+    optionally run whenever a new document is imported for a papis entry,
    if set in the plugin configuration.
    """
    documents = papis.cli.handle_doc_folder_query_all_sort(
        query, doc_folder, sort_field=None, sort_reverse=False, _all=_all
@ -71,19 +87,22 @@ def main(
        logger.warning(papis.strings.no_documents_retrieved_message)
        return
-    run(documents, edit=manual, write=write, git=git)
+    formatter = formatters[template]
    run(documents, edit=manual, write=write, git=git, formatter=formatter)
 def run(
    documents: list[Document],
    formatter: Formatter,
    edit: bool = False,
    write: bool = False,
    git: bool = False,
 ) -> None:
-
+    annotated_docs = extractor.start(documents)
    doc_annotations: list[AnnotatedDocument] = extractor.start(documents)
    if write:
-        exporter.to_notes(doc_annotations, edit=edit, git=git)
+        exporter.to_notes(
            formatter=formatter, annotated_docs=annotated_docs, edit=edit, git=git
        )
    else:
-        exporter.to_stdout(doc_annotations)
+        exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs)
--- a/papis_extract/annotation_data.py
+++ b/papis_extract/annotation_data.py
@ -20,7 +20,10 @@ COLORS = {
@dataclass
 class Annotation:
-    """A PDF annotation object"""
+    """A PDF annotation object.
    Contains all information necessary for the annotation itself, content and metadata.
    """
    file: str
    colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0))
@ -31,7 +34,7 @@ class Annotation:
    type: str = "Highlight"
    minimum_similarity_color: float = 1.0
-    def format(self, formatting):
+    def format(self, formatting: str, doc: Document = Document()):
        """Return a formatted string of the annotation.
        Given a provided formatting pattern, this method returns the annotation
@ -45,6 +48,7 @@ class Annotation:
            "page": self.page,
            "tag": self.tag,
            "type": self.type,
            "doc": doc,
        }
        return chevron.render(formatting, data)
@ -55,9 +59,7 @@ class Annotation:
        Finds the closest named color to the annotation and returns it,
        using euclidian distance between the two color vectors.
        """
-        annot_colors = (
+        annot_colors = self.colors or (0.0, 0.0, 0.0)
            self.colors or (0.0, 0.0, 0.0)
        )
        nearest = None
        minimum_similarity = (
            papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0
@ -83,5 +85,11 @@ class Annotation:
@dataclass
 class AnnotatedDocument:
    """Contains all annotations belonging to a single papis document.
    Combines a document with a list of annotations which belong to it."""
    document: Document
    annotations: list[Annotation]
    # TODO could implement a from_doc() static method to generate annotation list?
--- a/papis_extract/exporter.py
+++ b/papis_extract/exporter.py
@ -6,64 +6,41 @@ import papis.api
 import papis.git
 import papis.config
 import Levenshtein
 from papis_extract.annotation import AnnotatedDocument
-from papis_extract.annotation_data import AnnotatedDocument, Annotation
+from papis_extract.formatter import Formatter
 logger = papis.logging.get_logger(__name__)
-def _format_annotation(annotation: Annotation) -> str:
+def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None:
    note = f"NOTE: {annotation.content}" if annotation.content else ""
    return f"> {annotation.text}\n  {note}"
 def to_stdout(annots: list[AnnotatedDocument]) -> None:
    """Pretty print annotations to stdout.
    Gives a nice human-readable representations of
    the annotations in somewhat of a list form.
    Not intended for machine-readability.
    """
-    if not annots:
+    output: str = formatter(annotated_docs)
-        return
+    print(output.rstrip("\n"))
    for entry in annots:
        if not entry.annotations:
            continue
        title_decoration = (
            f"{'=' * len(entry.document.get('title', ''))}   "
            f"{'-' * len(entry.document.get('author', ''))}"
        )
        print(
            f"{title_decoration}\n{papis.document.describe(entry.document)}\n{title_decoration}\n"
        )
        for a in entry.annotations:
            print(_format_annotation(a))
        if entry != annots[-1]:
            print("\n")
-def to_notes(annots: list[AnnotatedDocument], edit: bool, git: bool) -> None:
+def to_notes(
    formatter: Formatter,
    annotated_docs: list[AnnotatedDocument],
    edit: bool,
    git: bool,
    force: bool,
 ) -> None:
    """Write annotations into document notes.
    Permanently writes the given annotations into notes
    belonging to papis documents. Creates new notes for
    documents missing a note field or appends to existing.
    """
-    if not annots:
+    for entry in annotated_docs:
-        return
+        formatted_annotations = formatter([entry]).split("\n")
-
+        if formatted_annotations:
-    for entry in annots:
+            _add_annots_to_note(entry.document, formatted_annotations, force=force)
        if not entry.annotations:
            continue
        formatted_annotations: list[str] = []
        for a in entry.annotations:
            formatted_annotations.append(_format_annotation(a))
        _add_annots_to_note(entry.document, formatted_annotations)
        if edit:
            papis.commands.edit.edit_notes(entry.document, git=git)
@ -73,11 +50,26 @@ def _add_annots_to_note(
    document: papis.document.Document,
    formatted_annotations: list[str],
    git: bool = False,
    force: bool = False,
 ) -> None:
-    """Append new annotations to the end of a note.
+    """
    Append new annotations to the end of a note.
-    Looks through note to determine any new annotations which should be
+    This function appends new annotations to the end of a note file. It takes in a
-    added and adds them to the end of the note file.
+    document object containing the note, a list of formatted annotations to be
    added, and optional flags git and force. If git is True, the changes will be
    committed to git. If force is True, the annotations will be added even if they
    already exist in the note.
    :param document: The document object representing the note
    :type document: class:`papis.document.Document`
    :param formatted_annotations: A list of already formatted annotations to be added
    :type formatted_annotations: list[str]
    :param git: Flag indicating whether to commit changes to git, defaults to False.
    :type git: bool, optional
    :param force:  Flag indicating whether to force adding annotations even if they 
        already exist, defaults to False.
    :type force: bool, optional
    """
    logger.debug("Adding annotations to note.")
    notes_path = papis.notes.notes_path_ensured(document)
@ -86,9 +78,9 @@ def _add_annots_to_note(
    with open(notes_path, "r") as file_read:
        existing = file_read.readlines()
-    new_annotations: list[str] = _drop_existing_annotations(
+    new_annotations: list[str] = []
-        formatted_annotations, existing
+    if not force:
-    )
+        new_annotations = _drop_existing_annotations(formatted_annotations, existing)
    if not new_annotations:
        return
@ -96,7 +88,8 @@ def _add_annots_to_note(
        # add newline if theres no empty space at file end
        if len(existing) > 0 and existing[-1].strip() != "":
            f.write("\n")
-        f.write("\n".join(new_annotations))
+        print(new_annotations)
        f.write("\n\n".join(new_annotations))
        f.write("\n")
        logger.info(
            f"Wrote {len(new_annotations)} "
@ -116,6 +109,14 @@ def _add_annots_to_note(
 def _drop_existing_annotations(
    formatted_annotations: list[str], file_lines: list[str]
 ) -> list[str]:
    """Returns the input annotations dropping any existing.
    Takes a list of formatted annotations and a list of strings
    (most probably existing lines in a file). If anny annotations
    match an existing line closely enough, they will be dropped.
    Returns list of annotations without duplicates.
    """
    minimum_similarity = (
        papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0
    )
@ -123,7 +124,9 @@ def _drop_existing_annotations(
    remaining: list[str] = []
    for an in formatted_annotations:
        an_split = an.splitlines()
-        if not _test_similarity(an_split[0], file_lines, minimum_similarity):
+        if an_split and not _test_similarity(
            an_split[0], file_lines, minimum_similarity
        ):
            remaining.append(an)
    return remaining
--- a/papis_extract/extractor.py
+++ b/papis_extract/extractor.py
@ -10,7 +10,7 @@ import papis.config
 import papis.document
 from papis.document import Document
-from papis_extract.annotation_data import Annotation, AnnotatedDocument
+from papis_extract.annotation import Annotation, AnnotatedDocument
 logger = papis.logging.get_logger(__name__)
@ -83,6 +83,7 @@ def extract(filename: Path) -> list[Annotation]:
 def is_pdf(fname: Path) -> bool:
    """Check if file is a pdf, using mime type."""
    return magic.from_file(fname, mime=True) == "application/pdf"
--- a/papis_extract/formatter.py
+++ b/papis_extract/formatter.py
@ -0,0 +1,94 @@
 from collections.abc import Callable
 from papis_extract.annotation import AnnotatedDocument
 Formatter = Callable[[list[AnnotatedDocument]], str]
 def format_markdown(
    docs: list[AnnotatedDocument] = [], atx_headings: bool = False
 ) -> str:
    template = (
        "{{#tag}}#{{tag}}\n{{/tag}}"
        "{{#quote}}> {{quote}}{{/quote}}{{#page}} [p. {{page}}]{{/page}}"
        "{{#note}}\n  NOTE: {{note}}{{/note}}"
    )
    output = ""
    for entry in docs:
        if not entry.annotations:
            continue
        heading = f"{entry.document['title']} - {entry.document['author']}\n"
        if atx_headings:
            output += f"# {heading}\n"
        else:
            title_decoration = (
                f"{'=' * len(entry.document.get('title', ''))}   "
                f"{'-' * len(entry.document.get('author', ''))}"
            )
            output += f"{title_decoration}\n" f"{heading}" f"{title_decoration}\n\n"
        for a in entry.annotations:
            output += a.format(template)
            output += "\n\n"
        output += "\n\n\n"
    return output.rstrip()
 def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str:
    return format_markdown(docs, atx_headings=True)
 def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str:
    return format_markdown(docs, atx_headings=False)
 def format_count(docs: list[AnnotatedDocument] = []) -> str:
    output = ""
    for entry in docs:
        if not entry.annotations:
            continue
        count = 0
        for _ in entry.annotations:
            count += 1
        d = entry.document
        output += (
            f"{d['author'] if 'author' in d else ''}"
            f"{' - ' if 'author' in d else ''}"  # only put separator if author
            f"{entry.document['title'] if 'title' in d else ''}: "
            f"{count}\n"
        )
    return output.rstrip()
 def format_csv(docs: list[AnnotatedDocument] = []) -> str:
    header: str = "type,tag,page,quote,note,author,title,ref,file"
    template: str = (
        '{{type}},{{tag}},{{page}},"{{quote}}","{{note}}",'
        '"{{doc.author}}","{{doc.title}}","{{doc.ref}}","{{file}}"'
    )
    output = f"{header}\n"
    for entry in docs:
        if not entry.annotations:
            continue
        d = entry.document
        for a in entry.annotations:
            output += a.format(template, doc=d)
            output += "\n"
    return output.rstrip()
 formatters: dict[str, Formatter] = {
    "count": format_count,
    "csv": format_csv,
    "markdown": format_markdown,
    "markdown_atx": format_markdown_atx,
    "markdown_setext": format_markdown_setext,
 }
--- a/poetry.lock
+++ b/poetry.lock
@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 [[package]]
 name = "arxiv2bib"
@ -183,6 +183,70 @@ files = [
    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 [[package]]
 name = "coverage"
 version = "7.3.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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    {file = "rapidfuzz-3.3.0.tar.gz", hash = "sha256:5e71bc5829f41e78b2d009431aedeb308ee3699d2bbbc68b7739db9b40bd1465"},
 ]
 [package.extras]
@ -883,13 +981,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 [[package]]
 name = "soupsieve"
-version = "2.4.1"
+version = "2.5"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
+    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
-    {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
+    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
 ]
 [[package]]
@ -939,13 +1037,13 @@ telegram = ["requests"]
 [[package]]
 name = "typing-extensions"
-version = "4.7.1"
+version = "4.8.0"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
+    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
-    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
+    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
 ]
 [[package]]
@ -980,7 +1078,7 @@ files = [
 name = "whoosh"
 version = "2.7.4"
 description = "Fast, pure-Python full text indexing, search, and spell checking library."
-optional = false
+optional = true
 python-versions = "*"
 files = [
    {file = "Whoosh-2.7.4-py2.py3-none-any.whl", hash = "sha256:aa39c3c3426e3fd107dcb4bde64ca1e276a65a889d9085a6e4b54ba82420a852"},
@ -988,7 +1086,10 @@ files = [
    {file = "Whoosh-2.7.4.zip", hash = "sha256:e0857375f63e9041e03fedd5b7541f97cf78917ac1b6b06c1fcc9b45375dda69"},
 ]
 [extras]
 whoosh = ["whoosh"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "a3af36ed2941235df158c20ba9b66bdf5a0af0554235fd004ec77c3e88def3c3"
+content-hash = "02d5ac314a19f14103372c7ceccdaec080df3fdc2fdb1381f2f6343cd6d17db4"
--- a/pyproject.toml
+++ b/pyproject.toml
@ -12,17 +12,21 @@ pymupdf = "^1.23.1"
 levenshtein = "^0.21.1"
 papis = "^0.13"
 click = "^8.1.7"
-whoosh = "^2.7.4"
+whoosh = { version = "^2.7.4", optional = true }
 python-magic = "^0.4.27"
 chevron = "^0.14.0"
 [tool.poetry.extras]
 whoosh = ["whoosh"]
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.0"
 coverage = "^7.3.1"
 pytest-cov = "^4.1.0"
 [tool.poetry.plugins."papis.command"]
 extract = "papis_extract:main"
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.0"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
--- a/tests/test_annotation.py
+++ b/tests/test_annotation.py
@ -1,5 +1,6 @@
 from papis.document import Document
 import pytest
-from papis_extract.annotation_data import Annotation
+from papis_extract.annotation import Annotation
@pytest.mark.parametrize(
@ -16,7 +17,7 @@ from papis_extract.annotation_data import Annotation
        ),
    ],
 )
-def test_formatting(fmt_string, expected):
+def test_formatting_replacements(fmt_string, expected):
    sut = Annotation(
        "myfile",
        text="I am the text value",
@ -25,13 +26,30 @@ def test_formatting(fmt_string, expected):
    assert sut.format(fmt_string) == expected
-def test_colorname_matches_exact():
+@pytest.mark.parametrize(
    "fmt_string,expected",
    [
        ("{{doc.title}}", "document-title"),
        ("{{doc.title}}-{{doc.author}}", "document-title-document-author"),
        ("{{quote}} ({{doc.author}})", "I am the text value (document-author)"),
    ]
 )
 def test_formatting_document_access(fmt_string, expected):
    sut = Annotation(
-        "testfile", colors=(1.0,0.0,0.0), minimum_similarity_color=1.0
+        "myfile",
        text="I am the text value",
        content="Whereas I represent the note",
    )
    doc = Document(data= {"title": "document-title", "author": "document-author"})
    assert sut.format(fmt_string, doc=doc) == expected
 def test_colorname_matches_exact():
    sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0)
    c_name = sut.colorname
    assert c_name == "red"
 # TODO inject closeness value instead of relying on default
@pytest.mark.parametrize(
    "color_value",
@ -44,8 +62,6 @@ def test_colorname_matches_exact():
    ],
 )
 def test_matches_inexact_colorname(color_value):
-    sut = Annotation(
+    sut = Annotation("testfile", colors=color_value, minimum_similarity_color=0.833)
        "testfile", colors=color_value, minimum_similarity_color=0.833
    )
    c_name = sut.colorname
    assert c_name == "red"
--- a/tests/test_formatting.py
+++ b/tests/test_formatting.py
@ -0,0 +1,80 @@
 from papis.document import Document
 from papis_extract.annotation import AnnotatedDocument, Annotation
 from papis_extract.formatter import (
    format_count,
    format_csv,
    format_markdown,
    format_markdown_atx,
    format_markdown_setext,
 )
 an_doc: AnnotatedDocument = AnnotatedDocument(
    Document(data={"author": "document-author", "title": "document-title"}),
    [
        Annotation("myfile.pdf", text="my lovely text"),
        Annotation("myfile.pdf", text="my second text", content="with note"),
    ],
 )
 md_default_output = """==============   ---------------
 document-title - document-author
 ==============   ---------------
 > my lovely text
 > my second text
  NOTE: with note"""
 def test_markdown_default():
    fmt = format_markdown
    assert fmt([an_doc]) == md_default_output
 def test_markdown_atx():
    fmt = format_markdown_atx
    assert fmt([an_doc]) == (
        """# document-title - document-author
 > my lovely text
 > my second text
  NOTE: with note"""
    )
 def test_markdown_setext():
    fmt = format_markdown_setext
    assert fmt([an_doc]) == md_default_output
 def test_count_default():
    fmt = format_count
    assert fmt([an_doc]) == ("""document-author - document-title: 2""")
 def test_csv_default():
    fmt = format_csv
    assert fmt([an_doc]) == (
        "type,tag,page,quote,note,author,title,ref,file\n"
        'Highlight,,0,"my lovely text","","document-author",'
        '"document-title","","myfile.pdf"\n'
        'Highlight,,0,"my second text","with note","document-author",'
        '"document-title","","myfile.pdf"'
    )
 # sadpath - no annotations contained for each format
 def test_markdown_no_annotations():
    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
    assert format_markdown([d]) == ""
 def test_count_no_annotations():
    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
    assert format_count([d]) == ""
 def test_csv_no_annotations():
    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
    assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file"
Author	SHA1	Message	Date
Marty Oehme	984025b472	feat: Add option to force-add annotations Some checks failed ci/woodpecker/push/test unknown status Details ci/woodpecker/push/lint Pipeline failed Details ci/woodpecker/push/static_analysis Pipeline failed Details Will turn off looking for duplicate annotations and simply add all.	2023-10-17 22:01:41 +02:00
Marty Oehme	14f1b9e75c	test: Add poetry-cov library	2023-10-17 21:16:40 +02:00
Marty Oehme	c9736a5f32	test: Add tests for formatter sad paths	2023-10-12 19:27:16 +02:00
Marty Oehme	f67ac8cdb3	chore: Fix markdown lint issues	2023-10-12 19:26:41 +02:00
Marty Oehme	2700e4adc3	test: Add code coverage dev dependency	2023-09-22 21:53:55 +02:00
Marty Oehme	1e29642cba	test: Fix formatting and annotation tests	2023-09-22 21:49:52 +02:00
Marty Oehme	ee4690f52b	feat: Add atx-style markdown Added markdown with atx style headers, can be chosen as alternative markdown template on the cli. The existing 'markdown' template will still default to setext-style headers.	2023-09-21 22:05:39 +02:00
Marty Oehme	7ee8d4911e	refactor: Make formatters functions Formatters have been classes so far which contained some data (the tamplate to use for formatting and the annotations and documents to format) and the actual formatting logic (an execute function). However, we can inject the annotations to be formatted and the templates so far are static only, so they can be simple variables (we can think about how to inject them at another point should it come up, no bikeshedding now). This way, we can simply pass around one function per formatter, which should make the code much lighter, easier to add to and especially less stateful which means less areas of broken interactions to worry about.	2023-09-21 21:54:24 +02:00
Marty Oehme	929e70d7ac	chore: Update poetry.lock	2023-09-21 19:36:00 +02:00
Marty Oehme	31b878c9eb	refactor: Move Annotations into annotation module	2023-09-20 17:22:29 +02:00
Marty Oehme	3670f70319	docs: Add formatting documentation Added documentation on using output templates and that they will invalidate the 'existing' annotation search.	2023-09-20 09:15:00 +02:00
Marty Oehme	e511ffa48d	feat: Add CSV formatter Added formatter for csv-compatible syntax. The formatting is quite basic with no escaping happening should that be necessary. However, for an initial csv output it suffices for me.	2023-09-20 09:15:00 +02:00
Marty Oehme	5f0bc2ffad	feat: Add count formatter Added formatter which counts and outputs the number of annotations in each document.	2023-09-20 09:14:59 +02:00
Marty Oehme	5a6d672c76	refactor: Move formatting logic to formatters Formatters (previously templates) were pure data containers before, continating the 'template' for how things should be formatted using mustache. The formatting would be done a) in the exporters and b) in the annotations. This spread of formatting has now been consolidated into the Formatter, which fixes the overall spread of formatting code and now can coherently format a whole output instead of just individual annotations. A formatter contains references to all documents and contained annotations and will format everything at once by default, but the formatting function can be invoked with reference to a specific annotated document to only format that. This commit should put more separation into the concerns of exporter and formatter and made formatting a concern purely of the formatters and annotation objects.	2023-09-20 09:14:58 +02:00
Marty Oehme	66f937e2a8	test: Add local papis settings for testing	2023-09-20 09:14:55 +02:00
Marty Oehme	cbe2e7cb03	feat: Allow cli option for template choice	2023-09-20 09:14:54 +02:00
Marty Oehme	9674592a9f	docs: Add developer notes to README	2023-09-20 09:14:43 +02:00
Marty Oehme	07d4de9a46	docs: Add docstrings	2023-09-20 09:13:04 +02:00
Marty Oehme	4eb983d9e3	refactor: Move templating to separate file	2023-09-20 09:12:59 +02:00
Marty Oehme	e633c0335e	chore: Make whoosh database optional dependency	2023-09-20 09:12:54 +02:00
Marty Oehme	5450776eb2	refactor: Extract templating to model module	2023-09-20 09:12:45 +02:00
Marty Oehme	e56f014136	Add formatting style Markdown	2023-08-31 21:40:17 +02:00